Re: [modeller_usage] modeling of phosphorylated polypeptide
To: Dibyabhaba Pradhan <>
Subject: Re: [modeller_usage] modeling of phosphorylated polypeptide
From: Modeller Caretaker <>
Date: Tue, 11 Nov 2008 22:36:13 -0800
Dibyabhaba Pradhan wrote:
> I modelled number of proteins by basic modelling. After basic
> modelling during procheck evaluation the residues in most favorable
> region is generally above 90% but after loop refinement the residues
> in most favorable region comes below 90%. Please kindly inform me what
> may be the region for this.
> Also after energy minimization the the percentage of residue in most
> favorable region decreses.
I'm not sure what this has to do with phosphorylation, but there is
certainly no guarantee that a single minimization will give a "better"
model. You'd be better off building several models to get a reasonable
sampling of the energy landscape and then picking the best cluster or
Ben Webb, Modeller Caretaker
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